An estimate for the number of existing microbial species11,12 is 105–106, but only several thousand have been isolated in pure culture13. Thus, the majority of microorganisms from the environment resist cultivation in the laboratory. These “uncultivables” represent 99–99.99% of all microbial species in nature1-3. Phylogenetic analyses of rRNA sequences, particularly 16s rRNA sequences., obtained from direct sampling of environments suggest that uncultivated organisms can be found in nearly every taxon within the Bacteria and Archaea, and several groups at the division level have been identified with no known cultivable representatives4-10.
The principal reason for this disparity is that few microorganisms from environmental samples grow on nutrient media in Petri dishes. The discrepancy between the microbial total count and plate count is several orders of magnitude4-10, 14-16. Attempts to improve the recovery of microorganisms from environmental samples by manipulating growth media have been of limited success3,15,17,18, and the phenomenon of uncultivability has become known as the “great plate count anomaly.”19 Methods of isolating and growing previously uncultivable microorganisms are clearly desirable. Such methods would transform microbiology by opening up access to the bulk of microbial diversity, thereby revolutionizing drug discovery.